A couple of months ago I recommended a friend to buy Nikon D60 because it was on sale at the time he was going to buy himself a DSLR. Shortly after, I recommended another friend to buy a Sony A200 because of the same reason (was on sale at the time). While they were bringing some of their questions to me, I also had the chance to play with their cameras.
I think both are comparable in AF, exposure and flash performance with little differences or advantages/disadvantages. However, I found D60 being non-intuitive to use. I had to ask my friend how to do exposure or flash exposure compensation or change some other settings. It is also much more menu oriented to change settings making it a slower camera. A200 was on the other hand quite intuitive to learn to use without reading the manual.
Of course, one can always use no matter what camera after reading the instruction manual. But I put a positive value into being 'intuitive' which should means one can figure things out more easily and I think A200 wins in this respect. It has a function button which makes having quick and easy access to the secondary main functions of the camera (white balance, exposure compensation, etc.).
Aside from that, having image stabilization in the camera body is another very important bonus.
As per flash, I currently use Nikon D300 and a SB-800 and I have to say, I am not impressed with the flash performance of this combo at all. Don't get me wrong, D300 is a great camera but what I am personally experiencing is far from the positive stories I had read about the Nikon flash system. I only imagine D60 can't be better than D300.
So which one to go? If it was me, I would go for the one that is less expensive. If A300 is on sale, I would go for that one instead (because it also has live view though I don't know if I would use it at all).